Spinal cord data#

Morphometry#

Code imports#

# Python imports 
from IPython.display import clear_output
from pathlib import Path
import numpy as np
import pandas as pd

# Import custom tools
from tools.data import Data
from tools.plot import Plot

Download data#

data_type = 'spine'
release_version = 'latest'

dataset = Data(data_type)
dataset.download(release_version)
--2022-08-04 22:25:20--  https://github.com/courtois-neuromod/anat-processing/releases/download//r20220804/spinalcord_results.zip
Resolving github.com (github.com)... 140.82.113.3
Connecting to github.com (github.com)|140.82.113.3|:443... connected.
HTTP request sent, awaiting response... 
Archive:  spinalcord_results.zip
  inflating: data/spine/DWI_RD.csv   
  inflating: data/spine/DWI_FA.csv   
  inflating: data/spine/csa-SC_T2w.csv  
  inflating: data/spine/DWI_MD.csv   
  inflating: data/spine/MTR.csv      
  inflating: data/spine/MTsat.csv    
  inflating: data/spine/csa-GM_T2s.csv  
  inflating: data/spine/csa-SC_T1w.csv  
  inflating: data/spine/T1.csv       
302 Found
Location: https://objects.githubusercontent.com/github-production-release-asset-2e65be/333825187/c7568fab-84d3-45d2-950a-09ca065b1495?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20220804%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20220804T222520Z&X-Amz-Expires=300&X-Amz-Signature=f7a55e43949085913af6a306a89ba72b69ea220d6ef57b0ed2fa175469e34992&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=333825187&response-content-disposition=attachment%3B%20filename%3Dspinalcord_results.zip&response-content-type=application%2Foctet-stream [following]
--2022-08-04 22:25:20--  https://objects.githubusercontent.com/github-production-release-asset-2e65be/333825187/c7568fab-84d3-45d2-950a-09ca065b1495?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20220804%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20220804T222520Z&X-Amz-Expires=300&X-Amz-Signature=f7a55e43949085913af6a306a89ba72b69ea220d6ef57b0ed2fa175469e34992&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=333825187&response-content-disposition=attachment%3B%20filename%3Dspinalcord_results.zip&response-content-type=application%2Foctet-stream
Resolving objects.githubusercontent.com (objects.githubusercontent.com)... 185.199.109.133, 185.199.108.133, 185.199.111.133, ...
Connecting to objects.githubusercontent.com (objects.githubusercontent.com)|185.199.109.133|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 47607 (46K) [application/octet-stream]
Saving to: ‘spinalcord_results.zip’

     0K .......... .......... .......... .......... ......    100% 5.64M=0.008s

2022-08-04 22:25:21 (5.64 MB/s) - ‘spinalcord_results.zip’ saved [47607/47607]

Load data plot it#

dataset.num_sessions
dataset.load()

fig_spine = Plot(dataset, plot_name = 'spine-wm')

fig_spine.title = 'WM spinal cord morphometry'

White matter#

# If you're running this notebook in a Jupyter Notebook (eg, on MyBinder), change 'jupyter-book' to 'notebook'
fig_spine.display('jupyter-book', fig_id = 'spine-csa-wm')

Grey matter#

fig_spine = Plot(dataset, plot_name = 'spine-gm')

fig_spine.title = 'GM spinal cord morphometry'
# If you're running this notebook in a Jupyter Notebook (eg, on MyBinder), change 'jupyter-book' to 'notebook'
fig_spine.display('jupyter-book', fig_id = 'spine-csa-gm')

Quantitative MRI#

White matter#

data_type = 'qmri'
release_version = 'latest'

dataset = Data(data_type)
dataset.download(release_version)
--2022-08-04 22:25:22--  https://github.com/courtois-neuromod/anat-processing/releases/download//r20220804/spinalcord_results.zip
Resolving github.com (github.com)... 140.82.113.3
Connecting to github.com (github.com)|140.82.113.3|:443... connected.
HTTP request sent, awaiting response... 302 Found
Location: https://objects.githubusercontent.com/github-production-release-asset-2e65be/333825187/c7568fab-84d3-45d2-950a-09ca065b1495?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20220804%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20220804T222520Z&X-Amz-Expires=300&X-Amz-Signature=f7a55e43949085913af6a306a89ba72b69ea220d6ef57b0ed2fa175469e34992&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=333825187&response-content-disposition=attachment%3B%20filename%3Dspinalcord_results.zip&response-content-type=application%2Foctet-stream [following]
--2022-08-04 22:25:22--  https://objects.githubusercontent.com/github-production-release-asset-2e65be/333825187/c7568fab-84d3-45d2-950a-09ca065b1495?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20220804%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20220804T222520Z&X-Amz-Expires=300&X-Amz-Signature=f7a55e43949085913af6a306a89ba72b69ea220d6ef57b0ed2fa175469e34992&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=333825187&response-content-disposition=attachment%3B%20filename%3Dspinalcord_results.zip&response-content-type=application%2Foctet-stream
Resolving objects.githubusercontent.com (objects.githubusercontent.com)... 185.199.109.133, 185.199.108.133, 185.199.111.133, ...
Connecting to objects.githubusercontent.com (objects.githubusercontent.com)|185.199.109.133|:443... connected.
HTTP request sent, awaiting response... 
Archive:  spinalcord_results.zip
  inflating: data/qmri/DWI_RD.csv    
  inflating: data/qmri/DWI_FA.csv    
  inflating: data/qmri/csa-SC_T2w.csv  
  inflating: data/qmri/DWI_MD.csv    
  inflating: data/qmri/MTR.csv       
  inflating: data/qmri/MTsat.csv     
  inflating: data/qmri/csa-GM_T2s.csv  
  inflating: data/qmri/csa-SC_T1w.csv  
  inflating: data/qmri/T1.csv        
200 OK
Length: 47607 (46K) [application/octet-stream]
Saving to: ‘spinalcord_results.zip’

     0K .......... .......... .......... .......... ......    100% 5.71M=0.008s

2022-08-04 22:25:22 (5.71 MB/s) - ‘spinalcord_results.zip’ saved [47607/47607]
dataset.load()
fig_spine = Plot(dataset, plot_name = 'spine-2')
fig_spine.title = 'Spinal cord qMRI measures'
# If you're running this notebook in a Jupyter Notebook (eg, on MyBinder), change 'jupyter-book' to 'notebook'
fig_spine.display('jupyter-book', fig_id = 'spine-qmri-wm')